Continued development of ChEBI towards better usability for the systems biology and metabolic modelling community

经过一个世纪对自然界越来越详细的研究，生成细胞内分子成分的“部件列表”，生物科学在过去十年中经历了范式转变，朝着将这些单个分子片段放在一起，以了解它们在整体背景下的相互作用的方向发展。正是这些相互作用产生了整个细胞过程，它们的研究被称为系统生物学。系统生物学汇集了关于细胞、基因和蛋白质的广泛信息，以及作用于这些生物结构和内部的小分子。在药物发现和工业生物技术等应用领域，它提供了一个整体的视角，旨在跟踪并最终模拟生物系统的整个功能。为了从如此庞大的不同数据集合中构建这样的整体模型，需要对来自许多不同数据库的单个信息单元进行集成。如此大量数据的集成只能通过计算来实现。为了促进顺利整合，细胞系统内的单个分子成分需要稳定和唯一的标识符。这些标识符由标准化机构和数据库提供商分配给基因、蛋白质或小分子等实体，并有效地允许对分子部件列表进行编目。除此之外，与人类相关的信息，如名称、化学和生物结构、关系和属性，也与数据库中的各种实体相关联，为软件工具和研究人员自己提供了可用的资源。数据库化学实体的生物利益（ChEBI）作为这样的信息资源和稳定的标识符在生物利益的小分子领域。ChEBI为生物科学界提供语义、生物和化学信息，以及与生物学相关的小化合物的稳定标识符，包括所谓的代谢物。代谢物是生物体内的小分子，涉及多种过程，包括为身体提供能量，作为组织的组成部分，在生物体内或生物之间充当防御或信号。出于这些目的，ChEBI在生物科学界被广泛使用，它向ChEBI团队发送分配特定小分子实体标识符的正式请求，然后ChEBI团队执行分配，将信息发布到公共领域并通知请求方请求已完成。当前提案的目的是进一步开发ChEBI资源并创建周边工具，以全面解决系统生物学和代谢建模社区的化学信息学（软件和数据）需求，以便他们反过来可以进一步实现他们的目标，即创建有意义的模拟和模型，使全系统研究能够应对紧迫的公共卫生和能源挑战。为了方便这种使用，我们建议：开发一个全面的软件库，以编程方式访问ChEBI，该软件库将适用于所有可用的主要操作系统；2 .扩展ChEBI数据库资源，以增强稳定性，增加社区参与，增加额外的生物学相关关系，并为分子实体的生物学背景提供新的强大可视化；在系统生物学研究中，将人类、小鼠、大肠杆菌和酵母等重要生物的所有已知代谢物纳入ChEBI。制作新的培训材料，并向社区提供培训课程。

After a century of studying nature in greater and greater detail, generating the "parts list" of the molecular components within the cell, the biological sciences have undergone a paradigm shift in the last decade, moving towards putting together these individual molecular pieces to understand their interactions in a holistic context. It is these interactions which give rise to overall cellular processes, and their study has has been termed systems biology.Systems biology brings together a wide range of information about cells, genes and proteins, as well as the small molecules that act on and within these biological structures. In the service of its application areas, such as drug discovery and industrial biotechnology, it gives a holistic perspective aiming to track and eventually simulate the entire functioning of biological systems. In order to build up such holistic models from such a vast collection of diverse data, integration of individual units of information from many diverse databases needs to be performed. This integration of such a high volume of data can only feasibly be performed computationally. To facilitate smooth integration, individual molecular components within the cellular system require stable and unique identifiers. These identifiers are assigned to entities such as genes, proteins or small molecules by standardization bodies and database providers, and effectively allow the molecular parts list to be catalogued. In addition to this, human-relevant information such as names and chemical and biological structures, relationships and properties are also associated with the various entities in the databases, providing resources that are useable by both software tools and researchers themselves.The database Chemical Entities of Biological Interest (ChEBI) acts as a resource for such information and stable identifiers in the area of small molecules of biological interest. ChEBI provides for the bioscientific community semantic, biological and chemical information as well as stable identifiers for small chemical compounds relevant in biology, including the so-called metabolites. Metabolites are small molecules in organisms that are implicated in diverse processes including supplying the body with energy, serving as building blocks for tissue, and acting as a defence or as a signal within the organism or between organisms. For these purposes, ChEBI is widely used in the bioscience community, which sends formal requests for the assignment of identifiers for particular small molecule entities to the ChEBI team, who then perform the assignment, publish the information into the public domain and inform the requesting party that the request has been fulfilled.The aim of the current proposal is to further develop the ChEBI resource and create surrounding tools towards comprehensively addressing the chemical informatics (software and data) needs of the systems biology and metabolic modelling communities, so that they in turn can further their objective to create meaningful simulations and models that enable whole-systems research into pressing public health and energy challenges. In order to facilitate this use, we propose to:1. Develop a comprehensive software library for accessing ChEBI programmatically which will work across all major available operating systems;2. Extend the ChEBI database resource to enhance stability, increase community involvement, add additional biologically relevant relationships, and provide a new powerful visualisation for the biological context of molecular entities;3. Curate into ChEBI all known metabolites across important organisms in systems biology studies: human, mouse, E. coli and yeast.4. Create new training materials and delivery of training courses to the community.